BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 01-11-2018, 04:07 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 18,201
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Solution NMR Structure and Backbone Dynamics of the Partially Disordered Arabidopsis thaliana Phloem Protein 16-1, A Putative mRNA Transporter.

Solution NMR Structure and Backbone Dynamics of the Partially Disordered Arabidopsis thaliana Phloem Protein 16-1, A Putative mRNA Transporter.

Solution NMR Structure and Backbone Dynamics of the Partially Disordered Arabidopsis thaliana Phloem Protein 16-1, A Putative mRNA Transporter.

Biochemistry. 2018 Jan 10;:

Authors: Sashi P, Singarapu KK, Bhuyan AK

Abstract
Although RNA-binding proteins in plant phloem are believed to carry out long-distance systemic transport of RNA in the phloem conduit, the structure of none of them is known. The Arabidopsis thaliana phloem protein 16-1 (AtPP16-1) is such a putative mRNA transporter whose structure and backbone dynamics have been studied at pH 4.1, 25oC, by high-resolution NMR spectroscopy. Results obtained using basic optical spectroscopic tools show that the protein is unstable with little secondary structure near the physiological pH of the phloem sap. Fluorescence-monitored titrations reveal that AtPP16-1 binds not only A. thaliana RNA (Kdiss ~ 67 nM) but also sheared DNA and model dodecamer DNA, albeit the affinity for DNA is ~15-fold less. In the solution structure of the protein secondary structural elements are formed of residues 3-9 (?1), 56-62 (?2), 133-135 (?3), and 96-110 (??-helix). Most of the rest of the chain segments is disordered. The N-terminal disordered regions (residues 10-55) form a small lobe, which conjoins the rest of the molecule via a deep and large irregular cleft that could have functional implications. The average order parameter extracted by model-free analysis of 15N relaxation and {1H}-15N heteronuclear NOE data is 0.66, suggesting less restricted backbone motion. The average conformational entropy of the backbone NH vectors is -0.31 cal mol-1 K-1. These results also suggest structural disorder in AtPP16-1.


PMID: 29320165 [PubMed - as supplied by publisher]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Structure and dynamics of an intrinsically disordered protein region that partially folds upon binding by chemical-exchange NMR.
Structure and dynamics of an intrinsically disordered protein region that partially folds upon binding by chemical-exchange NMR. Related Articles Structure and dynamics of an intrinsically disordered protein region that partially folds upon binding by chemical-exchange NMR. J Am Chem Soc. 2017 Aug 07;: Authors: Charlier C, Bouvignies G, Pelupessy P, Walrant A, Marquant R, Kozlov M, De Ioannes P, Bolik-Coulon N, Sagan S, Cortes P, Aggarwal AK, Carlier L, Ferrage F Abstract Many intrinsically disordered proteins (IDPs) and protein...
nmrlearner Journal club 0 08-07-2017 07:31 PM
Iron Binding Properties of Recombinant Class A ProteinDisulfide Isomerase from Arabidopsis thaliana
Iron Binding Properties of Recombinant Class A ProteinDisulfide Isomerase from Arabidopsis thaliana http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.6b01257/20170407/images/medium/bi-2016-012576_0008.gif Biochemistry DOI: 10.1021/acs.biochem.6b01257 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/1K5pummcmNs More...
nmrlearner Journal club 0 04-08-2017 10:57 AM
Water–Polysaccharide Interactions in the Primary Cell Wall of Arabidopsis thaliana from Polarization Transfer Solid-State NMR
Water–Polysaccharide Interactions in the Primary Cell Wall of Arabidopsis thaliana from Polarization Transfer Solid-State NMR Paul B. White, Tuo Wang, Yong Bum Park, Daniel J. Cosgrove and Mei Hong http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja504108h/aop/images/medium/ja-2014-04108h_0009.gif Journal of the American Chemical Society DOI: 10.1021/ja504108h http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/7abtnNxi-xg
nmrlearner Journal club 0 07-15-2014 09:25 AM
NMR assignment and secondary structure of the C-terminal DNA binding domain of Arabidopsis thaliana VERNALIZATION1.
NMR assignment and secondary structure of the C-terminal DNA binding domain of Arabidopsis thaliana VERNALIZATION1. NMR assignment and secondary structure of the C-terminal DNA binding domain of Arabidopsis thaliana VERNALIZATION1. Biomol NMR Assign. 2011 May 8; Authors: Mylne JS, Mas C, Hill JM VERNALIZATION1 (VRN1) is a multidomain DNA binding protein from Arabidopsis thaliana that is required for the acceleration of flowering time in response to prolonged cold treatment; a physiological process called vernalization. VRN1 is a 39*kDa protein...
nmrlearner Journal club 0 05-10-2011 05:11 PM
[NMR paper] NMR structure of the single QALGGH zinc finger domain from the Arabidopsis thaliana S
NMR structure of the single QALGGH zinc finger domain from the Arabidopsis thaliana SUPERMAN protein. Related Articles NMR structure of the single QALGGH zinc finger domain from the Arabidopsis thaliana SUPERMAN protein. Chembiochem. 2003 Mar 3;4(2-3):171-80 Authors: Isernia C, Bucci E, Leone M, Zaccaro L, Di Lello P, Digilio G, Esposito S, Saviano M, Di Blasio B, Pedone C, Pedone PV, Fattorusso R Zinc finger domains of the classical type represent the most abundant DNA binding domains in eukaryotic transcription factors. Plant proteins...
nmrlearner Journal club 0 11-24-2010 09:01 PM
[NMR paper] NMR solution structure of ATTp, an Arabidopsis thaliana trypsin inhibitor.
NMR solution structure of ATTp, an Arabidopsis thaliana trypsin inhibitor. Related Articles NMR solution structure of ATTp, an Arabidopsis thaliana trypsin inhibitor. Biochemistry. 2002 Oct 15;41(41):12284-96 Authors: Zhao Q, Chae YK, Markley JL The three-dimensional structure of the precursor form of the Arabidopsis thaliana trypsin inhibitor (ATT(p), GenBank entry Z46816), a 68-residue (approximately 7.5 kDa) rapeseed class proteinase inhibitor, has been determined in solution at pH 5.0 and 25 degrees C by multinuclear magnetic resonance...
nmrlearner Journal club 0 11-24-2010 08:58 PM
[NMR paper] Solution NMR structure and backbone dynamics of the major cold-shock protein (CspA) f
Solution NMR structure and backbone dynamics of the major cold-shock protein (CspA) from Escherichia coli: evidence for conformational dynamics in the single-stranded RNA-binding site. Related Articles Solution NMR structure and backbone dynamics of the major cold-shock protein (CspA) from Escherichia coli: evidence for conformational dynamics in the single-stranded RNA-binding site. Biochemistry. 1998 Aug 4;37(31):10881-96 Authors: Feng W, Tejero R, Zimmerman DE, Inouye M, Montelione GT The major cold-shock protein (CspA) from Escherichia...
nmrlearner Journal club 0 11-17-2010 11:15 PM
[NMR paper] Recombinant production of the p10CKS1At protein from Arabidopsis thaliana and 13C and
Recombinant production of the p10CKS1At protein from Arabidopsis thaliana and 13C and 15N double-isotopic enrichment for NMR studies. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Recombinant production of the p10CKS1At protein from Arabidopsis thaliana and 13C and 15N double-isotopic enrichment for NMR studies. Protein Expr Purif. 1999 Jun;16(1):144-51 Authors: Landrieu I, Casteels P, Odaert B, De Veylder L, Portetelle D, Lippens G, Van Montagu M, Inzé D The CKS1At...
nmrlearner Journal club 0 08-21-2010 04:03 PM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This Thread:

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is On
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2018, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 04:17 AM.


Map